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  Module: FCSParse
  
    &mdash; Documentation by YARD 0.8.2.1
  
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    <span class="title">FCSParse</span>
  

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    <div id="content"><h1>Module: FCSParse
  
  
  
</h1>

<dl class="box">
  
  
    
  
    
  
  
  
    <dt class="r1 last">Defined in:</dt>
    <dd class="r1 last">lib/fcsparse.rb<span class="defines">,<br />
  lib/fcsparse/fcsconst.rb,<br /> lib/fcsparse/fcsevent.rb</span>
</dd>
  
</dl>
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<h2>Overview</h2><div class="docstring">
  <div class="discussion">
    
<p>Contains all classes and constants for parsing FCS v3.x formatted files.</p>


  </div>
</div>
<div class="tags">
  

</div><h2>Defined Under Namespace</h2>
<p class="children">
  
    
  
    
      <strong class="classes">Classes:</strong> <span class='object_link'><a href="FCSParse/FCSEvent.html" title="FCSParse::FCSEvent (class)">FCSEvent</a></span>, <span class='object_link'><a href="FCSParse/FCSFile.html" title="FCSParse::FCSFile (class)">FCSFile</a></span>, <span class='object_link'><a href="FCSParse/FCSParam.html" title="FCSParse::FCSParam (class)">FCSParam</a></span>
    
  
</p>

  <h2>Constant Summary</h2>
  
    <dl class="constants">
      
        <dt id="H_VersionStart-constant" class="">H_VersionStart =
          <div class="docstring">
  <div class="discussion">
    
<p>byte offsets to the start and end of the version string</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='integer val'>0</span>
</pre></dd>
      
        <dt id="H_VersionEnd-constant" class="">H_VersionEnd =
          
        </dt>
        <dd><pre class="code"><span class='integer val'>5</span>
</pre></dd>
      
        <dt id="H_OffsetBlockLength-constant" class="">H_OffsetBlockLength =
          <div class="docstring">
  <div class="discussion">
    
<p>length of the block specifying the offsets of text, data, analysis sections</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='integer val'>8</span>
</pre></dd>
      
        <dt id="H_TextBlockOffsetStart-constant" class="">H_TextBlockOffsetStart =
          <div class="docstring">
  <div class="discussion">
    
<p>offsets to the start and end of the text section offset</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='integer val'>10</span>
</pre></dd>
      
        <dt id="H_TextBlockOffsetEnd-constant" class="">H_TextBlockOffsetEnd =
          
        </dt>
        <dd><pre class="code"><span class='integer val'>18</span>
</pre></dd>
      
        <dt id="H_DataBlockOffsetStart-constant" class="">H_DataBlockOffsetStart =
          <div class="docstring">
  <div class="discussion">
    
<p>offsets to the start and end of the data section offset</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='integer val'>26</span>
</pre></dd>
      
        <dt id="H_DataBlockOffsetEnd-constant" class="">H_DataBlockOffsetEnd =
          
        </dt>
        <dd><pre class="code"><span class='integer val'>34</span>
</pre></dd>
      
        <dt id="H_AnalysisBlockOffsetStart-constant" class="">H_AnalysisBlockOffsetStart =
          <div class="docstring">
  <div class="discussion">
    
<p>offsets to the start and end of the analysis section offset</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='integer val'>42</span>
</pre></dd>
      
        <dt id="H_AnalysisBlockOffsetEnd-constant" class="">H_AnalysisBlockOffsetEnd =
          
        </dt>
        <dd><pre class="code"><span class='integer val'>50</span>
</pre></dd>
      
        <dt id="T_SupplTextStartKeyword-constant" class="">T_SupplTextStartKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying offset to supplementary text section</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$BEGINSTEXT</span>
</pre></dd>
      
        <dt id="T_SupplTextEndKeyword-constant" class="">T_SupplTextEndKeyword =
          
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$ENDSTEXT</span>
</pre></dd>
      
        <dt id="T_AnalysisStartKeyword-constant" class="">T_AnalysisStartKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying offset to analysis section</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$BEGINANALYSIS</span>
</pre></dd>
      
        <dt id="T_AnalysisEndKeyword-constant" class="">T_AnalysisEndKeyword =
          
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$BEGINANALYSIS</span>
</pre></dd>
      
        <dt id="T_DataStartKeyword-constant" class="">T_DataStartKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying offset to data section</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$BEGINDATA</span>
</pre></dd>
      
        <dt id="T_DataEndKeyword-constant" class="">T_DataEndKeyword =
          
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$ENDDATA</span>
</pre></dd>
      
        <dt id="T_ModeKeyword-constant" class="">T_ModeKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying the data mode</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$MODE</span>
</pre></dd>
      
        <dt id="T_DatatypeKeyword-constant" class="">T_DatatypeKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying the data type (e.g. integer, float, etc)</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$DATATYPE</span>
</pre></dd>
      
        <dt id="T_ByteorderKeyword-constant" class="">T_ByteorderKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying byte order and value when little endian</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$BYTEORD</span>
</pre></dd>
      
        <dt id="T_LittleEndianByteorder-constant" class="">T_LittleEndianByteorder =
          
        </dt>
        <dd><pre class="code"><span class='string val'>&quot;1,2,3,4&quot;</span>
</pre></dd>
      
        <dt id="T_ParameterCountKeyword-constant" class="">T_ParameterCountKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying the number of parameters measured per event</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$PAR</span>
</pre></dd>
      
        <dt id="T_EventCountKeyword-constant" class="">T_EventCountKeyword =
          <div class="docstring">
  <div class="discussion">
    
<p>keyword specifying total number of events</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='symbol val'>:$TOT</span>
</pre></dd>
      
        <dt id="T_ParameterNameKeywordRegex-constant" class="">T_ParameterNameKeywordRegex =
          <div class="docstring">
  <div class="discussion">
    
<p>regular expressions matching names and ranges of all parameters</p>


  </div>
</div>
<div class="tags">
  

</div>
        </dt>
        <dd><pre class="code"><span class='regexp val'>/P(\d+)N/</span>
</pre></dd>
      
        <dt id="T_ParameterRangeKeywordRegex-constant" class="">T_ParameterRangeKeywordRegex =
          
        </dt>
        <dd><pre class="code"><span class='regexp val'>/P(\d+)R/</span>
</pre></dd>
      
    </dl>
  







  
    <h2>
      Class Method Summary
      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
    </h2>

    <ul class="summary">
      
        <li class="public ">
  <span class="summary_signature">
    
      <a href="#process_file-class_method" title="process_file (class method)">+ (Object) <strong>process_file</strong>(filename, data_header_row = true) </a>
    

    
  </span>
  
  
  
  
  
  
  

  
    <span class="summary_desc"><div class='inline'>
<p>Processes a specified FCS-formatted file, and writes human-readable output
to disk in the format specified by <span class='object_link'><a href="FCSParse/FCSFile.html#write_metadata_and_data-instance_method" title="FCSParse::FCSFile#write_metadata_and_data (method)">FCSFile#write_metadata_and_data</a></span>.</p>
</div></span>
  
</li>

      
    </ul>
  



  <div id="class_method_details" class="method_details_list">
    <h2>Class Method Details</h2>

    
      <div class="method_details first">
  <h3 class="signature first" id="process_file-class_method">
  
    + (<tt>Object</tt>) <strong>process_file</strong>(filename, data_header_row = true) 
  

  

  
</h3><div class="docstring">
  <div class="discussion">
    
<p>Processes a specified FCS-formatted file, and writes human-readable output
to disk in the format specified by <span class='object_link'><a href="FCSParse/FCSFile.html#write_metadata_and_data-instance_method" title="FCSParse::FCSFile#write_metadata_and_data (method)">FCSParse::FCSFile#write_metadata_and_data</a></span>.</p>

<p>the data file should have a header row with the name of each column’s 
parameter.  Defaults to true.</p>


  </div>
</div>
<div class="tags">
  <p class="tag_title">Parameters:</p>
<ul class="param">
  
    <li>
      
        <span class='name'>filename</span>
      
      
        <span class='type'>(<tt>String</tt>)</span>
      
      
      
        &mdash;
        <div class='inline'>
<p>the filename of the FCS-encoded file (with path as required to locate it)</p>
</div>
      
    </li>
  
    <li>
      
        <span class='name'>data_header_row</span>
      
      
        <span class='type'>(<tt>Boolean</tt>)</span>
      
      
        <em class="default">(defaults to: <tt>true</tt>)</em>
      
      
        &mdash;
        <div class='inline'>
<p>an optional parameter specifying whether</p>
</div>
      
    </li>
  
</ul>


</div><table class="source_code">
  <tr>
    <td>
      <pre class="lines">


345
346
347
348
349
350
351
352
353</pre>
    </td>
    <td>
      <pre class="code"><span class="info file"># File 'lib/fcsparse.rb', line 345</span>

<span class='rubyid_def def kw'>def</span> <span class='rubyid_self self kw'>self</span><span class='dot token'>.</span><span class='rubyid_process_file identifier id'>process_file</span><span class='lparen token'>(</span><span class='rubyid_filename identifier id'>filename</span><span class='comma token'>,</span> <span class='rubyid_data_header_row identifier id'>data_header_row</span> <span class='assign token'>=</span> <span class='rubyid_true true kw'>true</span><span class='rparen token'>)</span>
  
  <span class='rubyid_fcsfile identifier id'>fcsfile</span> <span class='assign token'>=</span> <span class='rubyid_FCSFile constant id'>FCSFile</span><span class='dot token'>.</span><span class='rubyid_new_from_file identifier id'>new_from_file</span><span class='lparen token'>(</span><span class='rubyid_filename identifier id'>filename</span><span class='rparen token'>)</span>
  <span class='rubyid_fcsfile identifier id'>fcsfile</span><span class='dot token'>.</span><span class='rubyid_parse identifier id'>parse</span>
  <span class='rubyid_fcsfile identifier id'>fcsfile</span><span class='dot token'>.</span><span class='rubyid_write_metadata_and_data identifier id'>write_metadata_and_data</span><span class='lparen token'>(</span><span class='rubyid_data_header_row identifier id'>data_header_row</span><span class='rparen token'>)</span>
  
  <span class='rubyid_nil nil kw'>nil</span>
  
<span class='rubyid_end end kw'>end</span>
</pre>
    </td>
  </tr>
</table>
</div>
    
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